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Full R Bioconductor Training

Bioconductor is a free, open source and open development software project for the analysis and comprehension of genomic data generated by wet lab experiments in molecular biology. Bioconductor is based primarily on the statistical R programming language,

This 2 days full R Biocondcutor course will cover:

  1. DNA Blast
  2. Sequencing Using Bioconductor
  3. Extract Data from NCBI
  4. Databases in Bioconductor
  5. Microarray Analysis
  6. NGS Analysis
  7. Protein Analysis


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Course Code: CRS-N-0042586

Course Booking

$498.00

Course Date

Course Time

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Course Cancellation/Reschedule Policy

We reserve the right to cancel or re-schedule the course due to unforeseen circumstances. If the course is cancelled, we will refund 100% to participants.
Note the venue of the training is subject to changes due to class size and availability of the classroom.
Note the minimal class size to start a class is 3 Pax.


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Course Details

Day 1

Module 1 : Introduction to bioinformatics

  • What is bioinformatics
  • Types of online databases and online tools
  • Genomics resources
  • Protenomics resources


Module 2 : Introduction to bioConductor

  • BioConductor Website
  • installing BioConductor in R
  • Bioconductor packages, vignettes, tutorials
  • Bioconductor datasets(biocViews)

Module 3 : Databases in BioConductor

  • Annotation Hub
  • biomarts (online biomarts)
  • Genomic (full genomes)
  • GEOquery (NCBI Gene expression Omnibus) & ArrayExpress
  • KEGG (Kyto Encyclopedia for Genes and Genomes)
  • Gene libraries

Module 4 : Data files in BioConductor

  • Data containers
  • Importing data types
  • Downloading DNA
  • Manipulating DNA

Module 5: DNA Blast

  • NCBI blast 
  • Gene sequence blast
  • Protein blast

Module 6 : Ranges into BioConductor

  • Iranges
  • Granges
  • Granges plotting
  • Granges w genes

Day 2

Module 7: Visualizing Data in BioConductor

  • Visualizing genomic features
  • Visualizing DNA content
  • Visualizing gene expression

Module 8: Microarray Analysis

  • Expression sets 
  • Exploratory data analysis
  • Clustering
  • Linear Regression

Module 9: NGS Analysis

  • Working with shortread data
  • Filtering sequences
  • Matching and counting
  • Visualizing NGS

Module 10: Protein Analysis

  • Read Fasta file
  • Amino acid count
  • Compute isoelectric and Mw
  • Hydropathy scores

Module 11: Visualizing Genomes

  • ggbio package
  • Visualizing karyograms
  • Visualizing reference track
  • Visualizing ideogram
  • gvis package
  • genomegraphs package

Who Should Attend

This course is for the bioinformatics scientists, life science workers

Prerequisite

  • R programming
  • Molecular biology/biotechnology
  • Some bioinformatics would be helpful

Trainers

BioconductorTrainerDwight Nuwan Fonseka have a degree in Biotechnology (from NUS) ,Advanced diploma in Pharamceutical management (from MDIS) and Masters in Education (from NTU). He have 8 years experience of teaching biology at O and A levels/ IB level in international schools in Singapore and overseas.

BioinformaticsTrainerDr Brandon Ooi has a Bachelors degree in Computer Engineering and a PhD in Bioengineering from the National University of Singapore. He has published papers on machine learning, bioinformatics and microarray data analysis. He has six years of teaching experience at the polytechnic level and was also involved in the creation and teaching of modules for adult learners.

Bioinformatics TrainerDr. Marie Wong has a BSc (Biochemistry and Molecular Biology) from the University of Melbourne and a PhD (Structural Biology) from the University of Singapore. She has had more than 18 years in the field of Bioinformatics in both academic and industrial settings.

BioinformaticsTrainerDr Zheng Zejun has seven years’ experience in the data-mining field. Zejun worked as a (Sr.) bioinformatics scientist for six years and currently works as a data scientist manager. Dr. Zheng;s expertise covers machine learning, statistics, algorithm design, bioinformatics and high performance computing. He has published three machine learning algorithms on well-recognized academic journals together with the open source software (CUDA-CRISY, FSOM, DYSC). Zejun is professional with an extensive set of programming languages, including C/C++, Python, R, JAVA and flask for data driven analytics and scalable computing. He has also a broad knowledge of algorithms and mathematical models in the data-mining field.

Bioinformatics TrainerWesley Goi is currently in his final year of his PhD in Bioinformatics at National University of Singapore (NUS) where he previously received his degree in Molecular Biology at NUS (Honours 2nd Uppers). He was the TA for Introductory Bioinformatics LSM2241. He specialises in analysing high throughput DNA and RNA sequencing data of complex microbial communities using network analyses and various functional analyses. In his previous projects he has applied machine learning methods to vaccine discovery.

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